Gene expression programs are fundamental to all living processes. It is now possible to envision mapping the transcriptional regulatory networks that control gene expression programs in living cells. Such maps would be of fundamental value to biologists, and when extended to mammalian cells, might lead to new therapeutic strategies for human diseases. Recently developed technologies allow systematic identification of the genome-wide location of transcriptional regulatory proteins in living cells, and this information can be combined with gene expression and other information to discover transcriptional regulatory networks. We propose to further refine and automate the experimental and computational technologies that enable mapping of transcriptional regulatory networks in living cells. We will use these refined technologies to map the transcriptional regulatory networks that control major biological processes in living yeast cells, and to identify the issues that are key to large scale mapping of mammalian regulatory networks in future studies. The specific aims of this proposal are: 1) further refine and automate the experimental and analytical technologies that enable efficient mapping of transcriptional regulatory networks in living cells; 2) discover the transcriptional regulatory networks that control major biological processes in yeast, including cell cycle, nutrition, environmental response, genome maintenance, and development; 3) refine technologies necessary for mapping mammalian transcriptional regulatory networks and test them by initiating the mapping of regulatory networks involved in control of human cell cycle.